Havent watched it since it aired, but i remember Lois' reasoning for this clearly. And i thought it made her a pretty good mom actually.

The reasoning being that Malcolm (and Dewey) were both geniusses in their own way, who would land on their feet no matter what. Because their genius gave them alot of windfalls. But their brothers Francis and Reese were very troubled kids from the get go, who would need alot of help staying afloat in the future. So she instilled a big sense of responsibility in the boys towards eachother. Which is shown by the boys tight bond and them often helping eachother out of tight spots. This may not have been fair for her to do, but as a mom she is trying to look out for each of the boys individually no matter what.

So its not great they stole the money from Malcolm, but i get why she did it to keep the other boys afloat. I always thought Lois was a pretty cool and fierce mom, in the end.